The scan can only take place when the computer is turned on and there is no way to have it wake the computer to scan either.

If the scan is taking a long, long time, it could be for many reasons, extra large and full drives, many more compressed files than usual (whatever usual is!) as it has to unpack each one, scan and then repack.

You can alter the scanning parameters by opening SecurityCenter, click Virus and Spyware Protection to expand. Perhaps a good idea here would be turn off Scheduled Scanning and then always do a manual custom scan where you can tell it to ignore things.